Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
The GSC was established in 2005. It is an
open membership community working towards
better descriptions of our collection ...
Standards to support science http://gensc.org/
•Organizing meetings
•Forming working groups
•Creating Consensus Products

Standards to support science http://gensc.org/
“It is now clear that the full potential of sequence analysis can only be
achieved if the geographic and environmental con...
GSC 11,
Hinxton, 2010

Taking the „Common Path‟ towards
building consensus:
•Identify the problem
•Define a community to a...
Standards to support science http://gensc.org/
Standards

Standards to support science http://gensc.org/
Contextual data

Taxa
Habitat
Date and Time
Latitude/Longitude
Environmental measurements
DNA extraction method
Sequencing...
Standards to support science http://gensc.org/
Minimum Information about any Sequence (MixS)
• Minimum Information about a (Meta)Genome Sequence
MIGS/MIMS specifies a fo...
Please provide this minimum information when
you publish
•a genome
•a metagenome
•a marker gene study (e.g. ribosomal gene...
Item

submitted to insdc
investigation type
project name
geographic location (latitude and longitude)
geographic location ...
Yilmaz et al.
Nature Biotech.
2011; 29:415-420

Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Genes/OTUs

Environment (pH)

Standards to support science http://gensc.org/
In recent years, new sequencing
technologies have been
developed.
• Sequencing cost per base has
dropped rapidly
• Amount ...
Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Standards to support science http://gensc.org/
Linda Amaral-Zettler, MBL
Guy Cochrane, EMBL-EBI
Jim Cole, MSU
Neil Davies (Berkeley)
Peter Dawyndt, University of Ghent
D...
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The Genomic Standards Consortium - Minimum Information Checklists for Standardised Reporting of Metagenome Data - Peter Sterk

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- The Genomic Standards Consortium

- Reporting raw data and meta Minimum information checklists for standardised reporting of metagenome data data (contextual data)

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  • founding members of gsc were first to realize this problempromptly, in 2005, dawn field et al. were already writing perspective papers trying to explain how geolocation, time habitat contextual datatermed contextual data hereis important for understanding sequence collections
  • (First animation)When I started my work on mimarks, the gsc already had two published checklists; migs and mims for genomes and metagenomes(Second animation)With the development of mimarks, these two standards were extended and improved to cover phylogenetic and functional marker gene sequences as well(Third animation)Finally, there is another component called environmental packages, which were introduced during development of mimarksThese packages contain additional environmental and experimental parameters and organize them into large habitat boxes(Fourth animation)Finally, an umbrella framework to encompass all current and future gsc checklists was also established The idea of this framework is that all gsc checklists share a number of contextual data fields, such as geographical coordinates, controlled habitat description or some experimental related fieldsThen there are checklist specific fields, which are not shared by all checklists, but are specific to a certain type of sequence. In mimarks, this is for example target gene name(Fifth animation)To summarize the GSC checklists; there are currently three of them; migs, mims and mimarks, all collected under the framework of mixsThe goal of these checklists is to provide researchers with a structured and controlled means of enriching any kind of sequence data with environmental, geographic and experimental contextual data
  • The Genomic Standards Consortium - Minimum Information Checklists for Standardised Reporting of Metagenome Data - Peter Sterk

    1. 1. Standards to support science http://gensc.org/
    2. 2. Standards to support science http://gensc.org/
    3. 3. Standards to support science http://gensc.org/
    4. 4. The GSC was established in 2005. It is an open membership community working towards better descriptions of our collection of genomes, metagenomes and marker gene sets Standards to support science http://gensc.org/
    5. 5. Standards to support science http://gensc.org/
    6. 6. •Organizing meetings •Forming working groups •Creating Consensus Products Standards to support science http://gensc.org/
    7. 7. “It is now clear that the full potential of sequence analysis can only be achieved if the geographic and environmental context of the sequence data is considered, herewith referred to as contextual data” 7 Standards to support science http://gensc.org/
    8. 8. GSC 11, Hinxton, 2010 Taking the „Common Path‟ towards building consensus: •Identify the problem •Define a community to address it •Define scope of the solution •Implement solution •Gain adoption of solution GSC 12 Bremen, 2011 GSC 13 BGI 2012 GSC 14 Oxford, 2012 Standards to support science http://gensc.org/
    9. 9. Standards to support science http://gensc.org/
    10. 10. Standards Standards to support science http://gensc.org/
    11. 11. Contextual data Taxa Habitat Date and Time Latitude/Longitude Environmental measurements DNA extraction method Sequencing method Standards to support science http://gensc.org/
    12. 12. Standards to support science http://gensc.org/
    13. 13. Minimum Information about any Sequence (MixS) • Minimum Information about a (Meta)Genome Sequence MIGS/MIMS specifies a formal way to describe genomes/ metagenomes in more detail than is currently captured in public repository documents. • Minimum Information about a MARKer gene Sequence The MIMARKS checklist: 'electronic laboratory notebook' containing core contextual data items required for consistent reporting of marker gene investigations. MIMARKS uses the MIGS/MIMS checklists with respect to the nucleic acid sequence source and sequencing contextual data, but extends them with further experimental contextual data such as PCR primers and conditions, or target gene name. Standards to support science http://gensc.org/
    14. 14. Please provide this minimum information when you publish •a genome •a metagenome •a marker gene study (e.g. ribosomal genes) INSDC (DDBJ, ENA, GenBank) accept this information and encourage its submission to their public DNA databases Standards to support science http://gensc.org/
    15. 15. Item submitted to insdc investigation type project name geographic location (latitude and longitude) geographic location (country and/or sea,region) collection date environment (biome) environment (feature) environment (material) environmental package sequencing method BA EU PL VI ORG ME SU SP M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M M “M”=mandatory “C”=conditional mandatory “X”=recommended “-”=not applicable 15 Standards to support science http://gensc.org/
    16. 16. Yilmaz et al. Nature Biotech. 2011; 29:415-420 Standards to support science http://gensc.org/
    17. 17. Standards to support science http://gensc.org/
    18. 18. Standards to support science http://gensc.org/
    19. 19. Standards to support science http://gensc.org/
    20. 20. Genes/OTUs Environment (pH) Standards to support science http://gensc.org/
    21. 21. In recent years, new sequencing technologies have been developed. • Sequencing cost per base has dropped rapidly • Amount of sequence in INSDC database is currently doubling every 8 months • Democratisation of sequencing: bench top sequencers make technology available to individual labs Standards to support science http://gensc.org/
    22. 22. Standards to support science http://gensc.org/
    23. 23. Standards to support science http://gensc.org/
    24. 24. Standards to support science http://gensc.org/
    25. 25. Linda Amaral-Zettler, MBL Guy Cochrane, EMBL-EBI Jim Cole, MSU Neil Davies (Berkeley) Peter Dawyndt, University of Ghent Dawn Field, CEH (Chair of GSC) George Garrity, MSU Jack Gilbert, Argonne National Lab Frank Oliver Glöckner, MPI-Bremen Lynette Hirschman, MITRE Hans-Peter Klenk, DSMZ Renzo Kottmann, MPI-Bremen Rob Knight (University of Colorado Nikos Kyrpides, DOE, JGI Folker Meyer, Argonne National Lab Norman Morrison (University of Manchester) Inigo San Gil , LTER Susanna Sansone, University of Oxford Lynn Schriml, University of Maryland (Treasurer of GSC) Peter Sterk, GSC (Secretary of GSC) Dave Ussery DTU Owen White, University of Maryland John Wooley, UCSD (PI of RCN4GSC) Institutional Liasons to the GSC Board Ilene Mizrachi (NCBI/GenBank) Tatiana Tatusova (NCBI/RefSeq) Standards to support science http://gensc.org/

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